Contacts of the helix formed by residues 99 - 115 (chain D) in PDB entry 3GV5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 99 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 3.8 18.4 - - - +
59D GLN* 3.4 28.9 - - - +
96D GLY 3.4 10.5 - - - +
97D GLU 3.4 3.1 + - - +
98D ASP* 1.4 71.2 + - - +
100D THR* 1.3 58.4 + - - +
101D ARG 3.4 2.7 - - - -
102D TYR* 3.1 15.6 + - + +
103D ARG* 2.8 34.6 + - - +
125D PHE* 4.0 26.2 - - + -
873E G 5.5 0.4 - - - +
841F C 3.3 35.7 - - - +
842F T 3.7 27.0 + - - +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASP* 2.5 40.1 + - - +
99D LEU* 1.3 72.6 - - - +
101D ARG* 1.3 61.6 + - - +
103D ARG* 3.5 31.2 - - - +
104D GLU* 2.9 47.2 + - - +
304D GLU* 5.8 1.3 - - - +
331D ARG* 6.1 1.1 - - - -
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D VAL* 4.1 15.2 - - + +
43D GLU* 2.7 41.8 + - - -
46D SER* 3.1 28.0 + - - -
94D VAL* 5.5 0.6 - - - +
95D ASN 5.4 2.8 + - - -
98D ASP 4.9 5.6 + - - +
99D LEU 3.4 0.6 - - - -
100D THR* 1.3 79.3 + - - +
102D TYR* 1.3 73.0 + - + +
104D GLU* 4.0 11.8 - - - +
105D MSE 3.1 27.2 + - - +
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Residues in contact with TYR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PHE* 3.6 13.4 - - + -
39D TYR* 3.5 72.0 - + + -
42D VAL* 3.9 24.0 - - + -
43D GLU* 2.6 31.5 + - - +
57D VAL* 3.6 9.4 - - - +
95D ASN 4.5 0.2 + - - -
96D GLY* 3.4 34.6 - - - -
98D ASP 4.1 7.4 - - - -
99D LEU* 3.1 20.3 + - + +
101D ARG* 1.3 79.4 + - + +
103D ARG* 1.3 56.1 + - - +
105D MSE 3.4 1.3 + - - -
106D SER* 2.8 36.2 + - - -
125D PHE* 4.2 4.3 - - + -
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 2.8 19.6 + - - +
100D THR* 3.5 42.2 + - - +
102D TYR* 1.3 76.2 - - - +
104D GLU* 1.3 68.7 + - - +
106D SER* 3.3 6.3 - - - -
107D TYR* 3.1 49.6 + - + -
125D PHE* 3.8 28.7 - - + -
302D PHE* 6.1 0.7 - - - -
304D GLU* 4.0 4.8 + - - -
331D ARG* 3.2 62.3 - - - +
842F T 4.5 9.7 + - - -
843F C 4.2 4.8 + - - +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 2.9 34.9 + - - +
101D ARG* 4.0 12.8 - - - +
102D TYR 3.2 0.2 - - - -
103D ARG* 1.3 85.2 + - + +
105D MSE 1.3 59.0 + - - +
107D TYR* 3.4 6.8 + - - +
108D LYS* 3.0 30.1 + - + +
334D GLN* 4.7 15.2 + - - +
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Residues in contact with MSE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PHE* 3.8 15.5 - - + -
42D VAL* 4.0 19.7 - - + -
45D ILE* 3.8 26.0 - - + -
101D ARG 3.1 17.2 + - - +
102D TYR 3.8 3.1 - - - +
104D GLU* 1.3 73.1 - - - +
106D SER* 1.3 66.3 + - - +
108D LYS* 3.1 11.9 + - + +
109D VAL* 3.0 26.5 + - - +
191D LEU* 3.5 42.6 - - + +
193D LEU* 3.7 23.6 - - + -
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D PHE* 3.8 4.6 - - - -
102D TYR 2.8 18.8 + - - -
103D ARG* 3.3 11.2 - - - -
104D GLU 3.2 0.2 - - - -
105D MSE 1.3 76.4 - - - +
107D TYR* 1.3 60.7 - - - +
109D VAL* 3.3 9.2 + - - +
110D THR* 3.2 23.0 + - - -
122D ARG* 2.8 32.8 + - - -
125D PHE* 2.6 33.4 + - - +
128D ASN* 5.3 0.2 + - - -
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 3.1 45.1 + - + +
104D GLU* 3.4 5.6 + - - +
105D MSE 3.3 0.2 - - - -
106D SER* 1.3 73.2 - - - +
108D LYS* 1.3 58.7 + - + +
110D THR* 3.9 6.6 - - + +
111D GLU* 2.9 50.3 + - + +
122D ARG* 3.5 47.9 + - - +
125D PHE* 5.7 0.9 - + - -
297D GLY 4.2 13.0 + - - -
298D PRO* 5.2 0.7 - - + -
299D PRO* 3.5 40.6 - - + +
843F C 5.7 4.0 + - - -
844F A 5.4 0.5 + - - -
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLU* 3.0 21.3 - - + +
105D MSE 3.1 15.4 + - + +
107D TYR* 1.3 72.2 - - - +
109D VAL* 1.3 61.5 + - - +
111D GLU* 3.5 17.3 + - - +
112D LEU* 2.9 29.5 + - - +
191D LEU* 4.0 28.7 - - + +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 5.3 0.7 - - + -
35D LEU* 4.5 14.8 - - + -
38D PHE* 5.0 2.7 - - + -
105D MSE 3.0 16.7 + - - +
106D SER* 3.3 9.8 + - - +
108D LYS* 1.3 76.1 - - - +
110D THR* 1.3 63.4 + - - +
112D LEU* 3.1 6.3 + - - +
113D LEU* 3.0 30.8 + - + +
125D PHE 6.0 0.2 - - - +
126D ASP 5.9 0.7 - - - +
128D ASN* 3.7 20.0 - - - +
187D MSE 4.2 22.2 - - + -
191D LEU* 4.0 10.1 - - + -
193D LEU* 3.6 28.9 - - + -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D SER 3.2 4.1 + - - -
107D TYR* 3.9 11.7 - - + -
108D LYS 3.4 0.2 - - - -
109D VAL* 1.3 77.3 - - - +
111D GLU* 1.3 65.4 + - + +
113D LEU* 3.3 4.9 + - - +
114D GLU* 3.0 40.1 + - - +
120D VAL* 3.9 13.2 - - + +
122D ARG* 2.9 41.1 + - + +
128D ASN* 2.9 30.4 + - - +
296D SER* 5.7 1.8 - - - -
297D GLY 6.1 1.3 - - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D TYR* 2.9 39.2 + - + +
108D LYS* 3.8 19.1 - - - +
110D THR* 1.3 76.2 - - + +
112D LEU* 1.3 63.3 + - - +
114D GLU* 3.4 24.9 + - - +
115D GLU* 3.5 15.7 + - - +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D LYS 2.9 13.4 + - - +
109D VAL* 3.1 9.6 + - - +
111D GLU* 1.3 75.9 - - - +
113D LEU* 1.3 67.5 + - + +
115D GLU* 3.1 30.9 + - - +
116D PHE* 3.7 16.3 - - + -
183D MSE 4.3 1.3 - - - +
186D ALA* 3.7 34.1 - - + +
187D MSE 3.8 24.2 - - + -
190D GLN* 3.7 30.3 - - + +
191D LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 4.3 15.5 - - + -
109D VAL* 3.0 22.5 + - + +
110D THR 3.7 5.4 - - - +
112D LEU* 1.3 84.7 - - + +
114D GLU* 1.3 56.9 + - - +
115D GLU 3.1 0.2 - - - -
116D PHE* 2.8 30.6 + - - +
117D SER 3.3 5.7 + - - +
120D VAL* 3.9 14.1 - - + +
128D ASN* 3.4 44.9 - - + +
130D VAL* 4.3 8.5 - - + +
183D MSE 4.2 37.9 - - + +
187D MSE 4.4 11.0 - - - -
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D THR* 3.0 32.1 + - - +
111D GLU* 3.7 24.2 - - - +
112D LEU 3.3 0.4 - - - -
113D LEU* 1.3 74.7 - - - +
115D GLU* 1.3 59.6 + - - +
116D PHE 3.2 0.6 - - - -
117D SER 3.2 22.1 - - - +
118D PRO* 3.6 16.4 - - - +
120D VAL* 3.5 19.6 - - + +
295D LEU* 3.7 19.3 - - - +
297D GLY* 4.6 9.5 + - - -
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLU 3.5 14.1 + - - +
112D LEU* 3.2 20.9 - - - +
113D LEU 3.1 1.0 - - - -
114D GLU* 1.3 77.4 - - - +
116D PHE* 1.3 65.3 + - + +
190D GLN* 4.4 14.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il